Contents

1 Cellranger Illumina profiling (190c)

## [1] 27998   190
## [1] 27998   186

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 186
## Number of edges: 4045
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7919
## Number of communities: 4
## Elapsed time: 0 seconds

2 Cellranger Illumina profiling (951c)

## [1] 27998   951
## [1] 27998   935

## [1] 2000

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 935
## Number of edges: 25447
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8540
## Number of communities: 9
## Elapsed time: 0 seconds

3 Adding Nanopore data (ISOG/ISO)

4 Integration RNA

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 1121
## Number of edges: 31187
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8374
## Number of communities: 10
## Elapsed time: 0 seconds

5 Gene Markers Heatmap

6 Clusters re-labelling, saving .rds file

7 Gene markers

8 Heatmap

#Session Info

sessionInfo()
## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux buster/sid
## 
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
## 
## locale:
##  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
##  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
##  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] bindrcpp_0.2.2     metap_1.1          cowplot_0.9.4     
##  [4] ggrepel_0.8.0      xtable_1.8-3       knitr_1.21        
##  [7] RColorBrewer_1.1-2 forcats_0.4.0      stringr_1.3.1     
## [10] purrr_0.3.0        readr_1.3.1        tidyr_0.8.2       
## [13] tibble_2.0.1       ggplot2_3.1.0      tidyverse_1.2.1   
## [16] pheatmap_1.0.12    dplyr_0.7.8        Seurat_3.0.0.9000 
## [19] BiocStyle_2.10.0  
## 
## loaded via a namespace (and not attached):
##  [1] tsne_0.1-3          nlme_3.1-137        bitops_1.0-6       
##  [4] lubridate_1.7.4     httr_1.4.0          backports_1.1.3    
##  [7] tools_3.5.2         R6_2.3.0            irlba_2.3.3        
## [10] KernSmooth_2.23-15  lazyeval_0.2.1      colorspace_1.4-0   
## [13] withr_2.1.2         npsurv_0.4-0        tidyselect_0.2.5   
## [16] compiler_3.5.2      cli_1.0.1           rvest_0.3.2        
## [19] xml2_1.2.0          plotly_4.8.0        labeling_0.3       
## [22] bookdown_0.9        caTools_1.17.1.1    scales_1.0.0       
## [25] lmtest_0.9-36       ggridges_0.5.1      pbapply_1.4-0      
## [28] digest_0.6.18       rmarkdown_1.11      R.utils_2.8.0      
## [31] pkgconfig_2.0.2     htmltools_0.3.6     bibtex_0.4.2       
## [34] readxl_1.3.1        htmlwidgets_1.3     rlang_0.3.1        
## [37] rstudioapi_0.10     generics_0.0.2      bindr_0.1.1        
## [40] zoo_1.8-4           jsonlite_1.6        ica_1.0-2          
## [43] gtools_3.8.1        R.oo_1.22.0         magrittr_1.5       
## [46] Matrix_1.2-15       Rcpp_1.0.0          munsell_0.5.0      
## [49] ape_5.3             reticulate_1.11.1   R.methodsS3_1.7.1  
## [52] stringi_1.2.4       yaml_2.2.0          gbRd_0.4-11        
## [55] MASS_7.3-51.1       gplots_3.0.1.1      Rtsne_0.15         
## [58] plyr_1.8.4          grid_3.5.2          parallel_3.5.2     
## [61] gdata_2.18.0        listenv_0.7.0       crayon_1.3.4       
## [64] lattice_0.20-38     haven_2.1.0         splines_3.5.2      
## [67] hms_0.4.2           SDMTools_1.1-221    pillar_1.3.1       
## [70] igraph_1.2.4        future.apply_1.2.0  codetools_0.2-16   
## [73] glue_1.3.0          evaluate_0.12       lsei_1.2-0         
## [76] modelr_0.1.4        data.table_1.12.0   BiocManager_1.30.4 
## [79] png_0.1-7           Rdpack_0.10-1       cellranger_1.1.0   
## [82] gtable_0.2.0        RANN_2.6.1          future_1.12.0      
## [85] assertthat_0.2.0    xfun_0.4            rsvd_1.0.0         
## [88] broom_0.5.1         survival_2.43-3     viridisLite_0.3.0  
## [91] cluster_2.0.7-1     globals_0.12.4      fitdistrplus_1.0-14
## [94] ROCR_1.0-7